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Technically, it's only Wine, and VMware has it's own too. They're not recreating the API, the putting D3D through OpenGL. Pretty much the exact opposite of what you thought Microsoft was doing with Vista.
Doing it this was a wrapper doesn't violate any patents(at least to my knowledge.), but it's much less effective. Maybe if AMD and Nvidia also pitched in their efforts into Wine's D3D wrapper development would go faster, but I don't think they really care.

So Gallium will enable this to be done better, but it would be unwise for TG to actually /include/ Direct3D support in their own code?

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Ya, they only list Wine specifically, but seeing that they both share wine code and fall under the "clone" clause they could be sued as well unless they have some licensing agreement with MS already on their own.

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How exactly would microsoft stop AMD and nVidia from leaving Direct3D support in their drivers when they compile them for linux?

Unfortunately it's not that simple. Unlike with OpenGL, the D3D API is not implemented inside the driver itself. Microsoft write a huge part of the API themselves. This top layer routes commands to a much simpler interface which the drivers implement (in some ways similar to the way Gallium works). Without the Microsoft-controlled parts, the code in the drivers won't do much good.